Sexually antagonistic selection (or SAS) acts when an allele is beneficial to one sex but deleterious to the other. It is thought to be important to the maintenance of genetic diseases, variation in social behaviors, and evolution of genome structure. Despite its importance to evolution, we know little about the genomic impact of SAS in natural populations because the classical tools of molecular evolution cannot detect it. This project will advance our understanding of SAS in two dimensions: Aim 1 will use new methods to detect SAS by measuring the small differences between allele frequencies in males and females that result from SAS acting in the current generation. Individually, these differences are rarely statistically significant, but we recently discovered that these differences can be aggregated across the genome to detect and quantify SAS. We will apply this strategy to large samples of whole genomes from natural populations of stickleback fishes that differ in their degree of sexual dimorphism. The results will provide the first estimates of the genome-wide strength of SAS, and the total amount of mortality imposed on males and females because individuals carry alleles that are adapted to the other sex. Aim 2 will provide the first systematic test of the prevailing hypothesis that SAS drives transitions between XY and ZW sex chromosome systems. These transitions are key events in genome evolution: they rewire the sex determination pathway, can trigger the degeneration of the Y or W chromosome, and have downstream effects on population demography. While theory shows these transitions can result from SAS, no systematic test of the hypothesis has been carried out. The research will focus on poeciliid fishes that vary both within and between species for XY and ZW sex determination. A novel strategy will be used to obtain the phased sequences of X, Y, Z, and W chromosomes. Gene trees for these chromosomes will show the sequence in which they evolved, test a key prediction of the SAS hypothesis, and give unprecedented views of very young W sex chromosomes. The research will have two major kinds of broader impacts. (i) It will develop a new approach for detecting selection acting contemporaneously, and determining its demographic impact. The strategy is a major departure from current methods, which rely on genetic signatures that only accumulate over many generations. The new methods will have applications to diverse forms of selection and to other species, including humans. (ii) The project will develop poeciliid fishes as the first model system in which all four types of sex chromosomes (X, Y, Z, and W) can be studied. Important new research horizons will be opened, for example revealing how confining a sex chromosome to females (the W) alters the mode and tempo of its evolution.